Continuity mistake: Depending on the version, in the final confrontation between the Emperor and the Harkonnen, and Paul and the Fremen, you can see Thufir Hawat standing in the crowd of the imperial side. After the battle between Paul and Sting he has suddenly disappeared. This is due to there being different, much longer versions of the same film. There is a 120 minute version, 180 and 190 minutes, and apparently in Singapore you can buy a 240 minute version. However, in the long versions the stains on Thufir's lips and Paul's totally blue eyes do not appear in the extra scenes: now you see it, now you don't.
Deliberate mistake: The Fremen wear "stillsuits" to conserve their water, yet leave their heads completely uncovered. This would result in quite a bit of water loss through perspiration. (In the book, they wore hoods, masks and nose filters, leaving only the eyes uncovered, but it wouldn't work in a movie to have all the actor's faces obscured!).
Continuity mistake: The main character Paul is tied up on the floor next to his mother, who is also tied up. Paul tries to use his tied feet to fight, but is easily kicked back down to the floor. Then, very briefly, but , Paul is half unconscious with his arms NOT tied anymore, but next to his head. The next scene has Paul's arms tied up again and his mother says 'cut my son's bonds'. (00:11:25)
Revealing mistake: When the spice filled tank carrying the mutated Guild Navigator enters the hall where the Emperor is waiting, one of the Guild agents falls to the ground at the left side of the tank; first an arm trying to stop the fall and then the head are visible for a moment. (00:06:15)
Revealing mistake: In the extended version, when Dr. Yue receives the message from Baron Harkonen, one of the "dead" bodies in the background can be seen moving. (01:00:55)